The United States believes President Abdel Fattah Al-Sisi is still “continuing the democratic transition” in Egypt, State Department Deputy Spokeswoman Marie Harf said during a Monday press briefing.

This comes despite the US being “deeply disturbed” by the findings of Human Rights Watch’s (HRW) recently released report on the Egyptian government’s dispersal of the mass sit-in at Rabaa Al-Adaweya last summer.

The report, released on the dispersal’s one year anniversary on 14 August, alleged that the Egyptian government had carefully planned the operation in a way that disregarded civilian casualties. Harf noted that the State Department had in February produced its own Human Rights Report which also examined the Rabaa dispersal.

Despite US support for Al-Sisi’s efforts towards a democratic transition, Harf said Egypt has “a long way to go”, noting that part of the US’s aid to Egypt “has not been certified”.

In January 2014, the US Congress allocated $1.3bn for Egypt in the coming fiscal year, with $572m released in June. However, the January bill stipulated that the release of further aid is conditional upon democratic progress, including the holding of parliamentary elections.

“What we expect is the process that’s laid out by Egypt’s constitution… on how Egypt should be governed is adhered to, and that the government should take additional steps to allow for dissent, to allow for people to come out in the streets and make their voices heard if they’re doing so peacefully.”

The US will “say very clearly when he [Al-Sisi] needs to take more steps”, she added.

Harf said the US would “also continue pressing for the release of journalists and others … for politically motivated reasons.”

The US-Egyptian relationship has seen heightened tension since the ouster of former president Mohamed Morsi in July 2013.

In October 2013, the US partially suspended the delivery of military aid to Egypt in response to the latter’s crackdown on opposition. Harf was later asked in a 31 July press briefing why military aid to Israel had not been similarly suspended in light of mounting civilian casualties from the Israel Defense Force’s campaign in the Gaza Strip. The distinction, Harf said, was that the Egyptian government had been using the US aid “against its own people”.

The remarks prompted a response from the Egyptian foreign ministry, with Minister of Foreign Affairs Sameh Shoukry instructing the embassy in Washington to file a complaint, stating that the comments had “nothing to do with reality” and asserting that the statements issued by the spokespersons of the State Department should “reflect facts in the future”.

Despite these points of contention, Harf underlined that the two countries share a vital strategic partnership, first citing the “absolutely critical role” Egypt has played in cease-fire talks between Hamas and Israel, and in working towards a longer term truce, a goal she called “incredibly important regionally”.

She also cited US-Egyptian cooperation on counterterrorism, but qualified that “the title [of “terrorist”] can’t be used just to apply to anyone [those in the Egyptian government] don’t like. That can’t be applied to peaceful protesters. But we know there is a serious terrorist threat and we’re working with them on that.”

In instances of such “overlapping strategic interests”, Harf said the US and Egypt would work together, but added that this would not preclude criticism or disagreement.

“When we have concerns about what [the Egyptian government] has done, we will say so publicly and clearly, and also privately,” she said. “So it is a longstanding relationship, but one where, when we disagree, we are very clear about that. And this is certainly one of those cases.”